--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/modify/ob_addh.xml	Tue Mar 26 14:49:44 2013 -0400
@@ -0,0 +1,62 @@
+<tool id="ob_addh" name="Add hydrogen atoms" version="1.0">
+    <description>at a certain pH value</description>
+    <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command interpreter="python">
+    ob_addh.py
+      -i "${infile}"
+      --iformat "${infile.ext}"
+      -o "${outfile}"
+      $polar
+      --pH "${pH_value}"
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi" label="Select input file"/>
+        <param name="polar" type="boolean" truevalue="--polar" falsevalue="" label="Add hydrogens to polar atoms only"/>
+        <param name="pH_value" type="float" size="4" value="7.4" label="Specify pH value"/>
+    </inputs>
+    <outputs>
+        <data format_source="infile" name="outfile" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="CID_2244.can" ftype="smi" />
+            <param name="polar" value="--polar" />
+            <param name="pH_value" value="7.4" />
+            <output name="outfile" file="CID_2244_addh.can" ftype="can" />
+        </test>
+    </tests>
+    <help>
+
+.. class:: infomark
+
+**What does this tool do?**
+
+  This tool parses a molecular file and adds hydrogen atoms at a certain pH value.
+
+-----
+
+.. class:: infomark
+
+**Protocol:**
+
+  **1.** The hydrogen atoms included in the input molecule are deleted.
+
+  **2.** Protonation state is predicted at the target pH and the corresponding hydrogen atoms added accordingly.
+
+  **Hint:** to avoid possible crashes, only molecules with >5 heavy atoms are parsed.
+
+-----
+
+.. class:: infomark
+
+  **Output:** the output format is the same as the input format. 3D format files are required for this tool.
+
+-----
+
+**This tool uses Pybel:** N. M. O'Boyle, C. Morley and G. R. Hutchison. Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit Chem. Cent. J. 2008, 2, 5.
+
+    </help>
+</tool>